Some enzymes from the genus of Alicyclobacillus species are known such as described in Matzke et al.; Gene cloning, nucleotide sequence and biochemical properties of a cytoplasmic cyclomaltodexinase (neopullulanase) from Alicyclobacillus acidocalderius ATCC 2700; reclassification of a group of enzymes; Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases or Kolvula et al.; Cloning and sequencing of a gene encoding acidophilic amylase from Bacillus acidoceldarius. J. Gen. Microbiol. 139:2399 (1993) or Bartolucci et al.; Thioradoxin from Bacillus acidocaldarius: characterization, high-level expression in Escherichia coli and molecular modeling; Biochem. J. 328:277 (1997) or Tsuruoka et al.; Collagenolytic Serine-Carboxyl Proteinase from Alicyclobacillus sendainensis Strain NTAP-1: Purification, Characterization, Gene Cloning, and Heterologous Expression; Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases; Eckert K. & Schneider E., A thermoacidophilic endoglucanase (celB) from Alicyclobacillus acidocaldarius displays high sequence similarity to arabinofuranosidases belonging to family 51 of glycosyl hydrolases, Eur. J. Biochem., 270: 3593-3602, 2003.
In the pursuit of novel enzymes it is also known to screen for such new enzymes by subjecting potential candidates to specific enzyme assays. This approach is limited to the availability of enzyme assays and does not allow the identification of functional enzymes or polypeptides for which the activity is still unknown.
Further, whole genome sequencing is a known method to obtain the information on all genes from a given microorganism e.g. as described in Fleischmann et al.; Whole genome sequences and assembly of Haemophilus influenzae Rd; Nature 269: 496-512; (1995).
Most enzymes for industrial use are enzymes which are secreted to the medium by a microorganism. However, only a few percent of a microorganisms' genome encodes secreted proteins. For example only approx. 4% of the Bacillus subtilis genome or its closest relatives encode secreted proteins (van Diji et al.: Protein transport pathways in Bacillus subtilis: a genome-based road map; in “Bacillus subtilis and its closest relatives,”—From genes to cells; p. 337-355; A. L. Sonenshein (ed.); ASM Press 2002).
One disadvantage of genome sequencing is that the vast majority of the obtained sequences encode non secreted proteins.
Also known is signal trapping which is a method to identify genes including nucleotides encoding a signal peptide using a translational fusion to an extra cellular reporter gene lacking its own signal (WO 01/77315).